Development of a genome‐wide 200K SNP array and its application for high‐density genetic mapping and origin analysis of Camellia sinensis

作者：Kang Wei, Xinchao Wang, Xinyuan Hao, Yinhong Qian, Xin Li, Li-Yi Xu, Li Ruan, Yongxin Wang, Yazhen Zhang, Peixian Bai, Qiang Li, Shirin Aktar, Xili Hu, Guoyang Zheng, Liubin Wang, Liubin Wang, Benying Liu, Weizhong He, Hao Cheng, Liyuan Wang, Liyuan Wang · 发表于：Plant Biotechnology Journal · 年份：2021 · DOI：10.1111/pbi.13761 · 被引用次数：32 · 研究领域：Tea Polyphenols and Effects、Genetic Mapping and Diversity in Plants and Animals、Plant and Fungal Interactions Research

Tea is one of the most popular drinks in the world. It is a self-incompatible plant species, and its self-incompatibility greatly contributes to its high genetic diversity. Cultivated tea plants mainly include Camellia sinensis var. assamica (CSA) and Camellia sinensis var. sinensis (CSS). The former is characterized by large leaves, cold sensitive phenotype, and an arborous or semi-arborous habit, whereas CSS is characterized by smaller leaves, cold tolerance, and a shrub or semi-shrub growth habit. However, their genetic diversity and differentiation, especially the original relationship, still remain elusive. Earlier publications revealed a total of 218.9 million high-quality variants based on the chromosome-level reference genomes and re-sequencing data of tea plants (Wang et al., 2020). Following the SNP selection process, 5 360 472 SNPs were selected with minor allele frequencies >0.1. Then considering the genome-wide uniform distribution and location of SNPs on or close to genes, a set of 179 970 SNPs uniformly distributed across the genome were chosen for the development of the 200K Affymetrix Axiom SNP array. Relative information was deposited in the National Center for Biotechnology Information with accession number of GSE182082 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182082). All samples passed the quality assessment with an average call rate of 98.1%. The SNP reproducibility of duplicated samples was 99.71% for ‘LJ43’ and 99.67% for ‘BHZ’. The consi...